Freesurfer

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30081 discussions

Gyrification group comparison - GLM
by Georgia Kapizioni 10 May '21

10 May '21

External Email - Use Caution Dear FS experts, I am running a GLM for a group comparison (Healthy versus Patients) for gyrification, using the following command: mri_glmfit --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir which seems to work fine, however when I am running the mri_glmfit-sim command to correct my results, I am getting the following error, which is strange as I use smoothed data of 10 fwhm. Do you have any ideas why is this happening and how to resolve it? Thank you in advance, Best, Geo mri_glmfit-sim --glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs --cwp .05 --2spaces cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir SURFACE: fsaverage lh log file is lh.HDcvsCons1_pial.glmdir/cache.mri_glmfit-sim.log cd /Users/georgina/Downloads/HDf /Applications/freesurfer/bin/mri_glmfit-sim --glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs --cwp .05 --2spaces $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Mon May 10 00:10:37 EEST 2021 Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 georgina setenv SUBJECTS_DIR /Users/georgina/Downloads/HDf FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 43.252960 ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm43/abs/th13/mc-z.csd

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mri_preproc with ico < 7?
by Knut J Bjuland 10 May '21

10 May '21

External Email - Use Caution Dear Freesurfer experts, Is it possible to run mri_preproc with ico with lower than 7, for instance with ico equal to 4 or 5 in order to downsample the surface? (Since the surface is smoothed, it should be possible to downsample to save processing time when doing statistical modelling, right?) I tried using an --ico or --icoorder flag, but just got an error message. Are these functions not continued? Thank you Your Sincerely Knut Jørgen Bjuland, PhD

2 1

FA map registration to T1
by Russo, Andrew William 10 May '21

10 May '21

Hello FreeSurfer Developers, I am registering FA maps to T1 for a group of subjects with MS and in many cases the registration is poor for the anterior corpus callosum (attached), cerebellum, pons, and temporal lobe. I am using the following commands (FreeSurfer version 6.0): bbregister \ --dti \ --reg diff2T1_reg.dat \ --mov eddy_corrected_b0.nii.gz \ --s subject_temp mri_vol2vol \ --mov dtifit_FA.nii.gz \ --targ orig.mgz \ --o FA2T1.nii.gz \ --reg diff2T1_reg.dat Do you have any suggestions for improving this registration? Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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mri_label2_vol missing grey matter voxels
by Nakajima, Mitsuko 10 May '21

10 May '21

External Email - Use Caution Dear FreeSurfer Developers, I am trying to extract the cortical ROIs from my subjects. (1) mri_surf2surf, transform from fsaverage surface with Glasser atlas annotation, onto the subject surface. (2) mri_label2vol, transform from the subject's surface (labelled with the Glasser atlas) onto subject's volume. # Step 1: Transform from fsaverage to subject's surface (Ensure fsaverage contains HCP-MMP1.annot in labels folder) $ mri_surf2surf --srcsubject scripts/fsaverage --trgsubject ${i}/${sub} --hemi lh --sval-annot HCP-MMP1.annot --tval lh.HCP-MMP1_native.annot # Step2: Transform from subject's surface into your subject's volume $ mri_label2vol --temp ${SUBJECTS_DIR}/${i}/${sub}/mri/brain.mgz --annot HCP-MMP1_native.annot --o ${SUBJECTS_DIR}/${i}/${sub}/lh_native_glasser.nii.gz --hemi lh --subject ${i}/${sub} --regheader ${SUBJECTS_DIR}/${i}/${sub}/mri/aseg.mgz --proj frac 0 1 .1 --fillthresh .3 However, the output image shows pixelated grey matter. I've tried using different --filthresh, but the appearance remains the same. Please find attached the screenshot of the output, as well as the recon-all log. I've looked through the list, and I did not find a solution to a case that I can apply to my situation. 1) Freesurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: Mac OS X Mojave, 10.14.6 3) recon-all log as attached Thank you so much for your help. Kind regards, Mitsuko

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error while running mri_glmfit-sim command
by Paul, Rahul 10 May '21

10 May '21

Hi Freesurfer Experts, I am having some error while running mri_glmfit-sim command ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm56/abs/th20/mc-z.csd I was using the following command: mri_glmfit-sim --glmdir lh.class2_age.glmdir --cache 4 abs --cwp 0.05 --2spaces How can I fix the error? Thank you, Rahul

2 1

Extracting the entire brain mask from aparc+aseg.mgz
by Arman Avesta 10 May '21

10 May '21

External Email - Use Caution Hi gang, I have downloaded head MRIs of 1000 subjects from ADNI, together with their FreeSurfer generated aparc+aseg.mgz files. I'm using them in a 3D deep learning network. These MRIs are 256 x 256 x 256, which is too large for GPU training. Therefore, I'm trying to pre-process the volumes by putting a bounding box around the brain, crop the image, and then resize it to a smaller size (e.g. 64 * 100 * 100). To put the bounding box around the brain, I need the brain mask. I don't have access to the brainmasks of these subjects, so I'm trying to use mri_extract_label to make brainmasks for them. Is there a way to tell mri_extract_label to put together all labels in one volume? Best regards, Arman Arman Avesta, MD Radiology Resident & PhD Student Yale School of Medicine & Yale Graduate School of Arts and Sciences Email: arman.avesta(a)yale.edu

2 1

PET seeding with hippocampal subfields
by Mohammad Akradi 10 May '21

10 May '21

External Email - Use Caution Dear Freesurfer Development Team I've used freesurfer with hippocampal subfields module to get GM and Thickness in this region in detail. but now I need this subfields' mask to use it on my PET data. So I'll appreciate it if you tell me how I can get this regions' mask. Or which atlas I should use to achieve them? so I can calculate FDG uptake in these regions too. best regards -- Mohammad Akradi MSc Student, Institute of Medical Science and Technology, Shahid Beheshti University, Tehran, Iran

2 1

Native volume to fs_average surface
by Mason Wells 10 May '21

10 May '21

External Email - Use Caution Hi experts, I have some fMRI data that I have pre-processed in Feat. I want to resample a single subject's data to the fs_average surface but unsure of the most optimal way of doing this. At present I am warping the functional data to the MNI brain in the volume (using FSL's applywarp) and then resampling to fs_average using the following command. * mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh --hemi rh --mni152reg My question is whether you think this is the most appropriate approach, and/or if there is way to move directly from native volume to fs_average surface without needing to go via MNI volume? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1qGEoQnnU3besQKg-GQwdKq-WtCCzi1b5tl-HNLywYRQ48…><http://secure-web.cisco.com/1Mj4YBzh-BsbinaViI1QJ6drLVkixPOlMFL2tzAILihwp7N…> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Cortical surface analysis
by Ornaith O Reilly 10 May '21

10 May '21

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me. My goal is to be able to visualise electrodes contacts that are on lying on the cortical surface on a flat map and a spherical map. I've run recon-all and created the flatmap. I'm using Matlab to achieve this and I've loaded the information with the lines lhsphere = fs_read_surf( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere'); lhflatpatch=fs_read_patch( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D' ); 1. I want to be able to access the coordinates and show the electrons on the flat map/ sphere and I was wondering how to do this? I understand that the vertex ID number is what relates the coordinates in the original image to these surfaces. I am wondering how to access the vertex ID numbers ? At the moment I think that I only have access to the vertex coordinates and the vertex faces. 2. Additionally, I was wondering if there is a way to display the surface images through Matlab? What would be the best way to show the surface with the electrons overlaid on it? The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) I really appreciate any help with this as I'm really stuck. Thanks in advance for any help. Kind Regards, Ornaith O'Reilly

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Cannot select ROI edit tool in Freeview
by Mercy Mazurek 10 May '21

10 May '21

External Email - Use Caution I loaded my brainmask.mgz file generated from a "recon-all -autorecon1" command. When I open up Freeview, I see the icon but it is grayed out and I cannot select it to create a volume ROI on my image. How do I draw an ROI on my scans? Thanks for your help!

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